Well, just an update for the thread:

I got my bike fit properly today. Turns out the frame is actually too small for me (should be riding a 56, not a 51) and my seat was too high. So the seat was put down to a proper height and I got the handlebars extended out. The clips on my shoes were adjusted as well to sit on the actual ball of my foot.

Haven't had a chance to take it out riding yet (was raining with thunder and lightning all day here) but just spinning on the trainer in the store everything felt much better. I'm supposed to ride like I normally would this week and let them know on Friday how everything is going.

So, here's hoping for the best, but I am certainly optimistic!!

Thanks again for the advice, getting the bike fit was apparently an important step in solving my problem!